Resource
| Id | Histone_ChIP-seq/ENCSR000AKU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AKU [biosample_summary="Homo sapiens K562" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN221DTY|/analyses/ENCAN221DTY/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN221DTY|/analyses/ENCAN221DTY/} has in progress subobject document {5ff4d0e0-8492-491f-a224-34366a00de7f|/documents/5ff4d0e0-8492-491f-a224-34366a00de7f/} audit_not_compliant: Processed alignments file {ENCFF564SVK|/files/ENCFF564SVK/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 6873902 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed alignments file {ENCFF685PPQ|/files/ENCFF685PPQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 11454698 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF685PPQ|/files/ENCFF685PPQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF685PPQ|/files/ENCFF685PPQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.45. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AKU | float |
Histone_ChIP-seq_ENCSR000AKU |
Histone_ChIP-seq ENCSR000AKU [biosample_summary="Homo sapiens K562" and target="H3K4me3"]
|
 |
[2.08, 50.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 49967872 | 1.55% | 43357 |
| chr1 | 5246975 | 2.11% | 4417 |
| chr2 | 3397920 | 1.40% | 2959 |
| chr3 | 2907411 | 1.47% | 2550 |
| chr4 | 1962924 | 1.03% | 1655 |
| chr5 | 2257641 | 1.24% | 1896 |
| chr6 | 3387748 | 1.98% | 2747 |
| chr7 | 2570322 | 1.61% | 2266 |
| chr8 | 1903163 | 1.31% | 1692 |
| chr9 | 1904985 | 1.38% | 1713 |
| chr10 | 2177241 | 1.63% | 1906 |
| chr11 | 2664408 | 1.97% | 2269 |
| chr12 | 2643177 | 1.98% | 2231 |
| chr13 | 843129 | 0.74% | 772 |
| chr14 | 1508624 | 1.41% | 1360 |
| chr15 | 1589329 | 1.56% | 1368 |
| chr16 | 1916629 | 2.12% | 1667 |
| chr17 | 2742577 | 3.29% | 2369 |
| chr18 | 764108 | 0.95% | 701 |
| chr19 | 3085170 | 5.26% | 2711 |
| chr20 | 1320096 | 2.05% | 1223 |
| chr21 | 562777 | 1.20% | 492 |
| chr22 | 1049009 | 2.06% | 965 |
| chrX | 1562509 | 1.00% | 1428 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 43357 | 175 | 20018 | 1152.48 | 754 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF689QIJ.bed.gz | 1.06 MB | 5dea2993c0831ae344a989d601c09178 |
| ENCFF689QIJ.tabix.bed.gz | 478.05 KB | a16a515f2b44b2b224c3e9eb278bcc00 |
| ENCFF689QIJ.tabix.bed.gz.tbi | 185.13 KB | 76189a548aa452d290636f93764c36da |
| genomic_resource.yaml | 4.06 KB | bf7622a9958ed78045a28cd607058bb0 |
| statistics/ |